August 21, 2017

New Microbiome Digest and many many interesting articles: metagenome analysis as a powerful tool for enzyme bioprospecting, application of DGGE on oral bacterial community; labeling of prokaryotic mRNA in live cells with FISH-TAMB…
While in non-microbiology picks read and join very interesting project Scientist Selfies. This project explores how scientists use Instagram and how scientists’ IG posts can potentially change public perceptions of scientists’.

Events and jobs

Postdoc position for Cell Factory Construction, Novozymes, Denmark

IBS-Nature Conference on Frontiers in Genome Engineering

General microbiome

Genetic cargo and bacterial species set the rate of vesicle-mediated horizontal gene transfer – Frances Tran – Scientific Reports

Review: Archaea Are Interactive Components of Complex Microbiomes – Christine Moissl-Eichinger – Trends in Microbiology

 

Pregnancy and early life

Human Milk Oligosaccharides Exhibit Antimicrobial and Antibiofilm Properties against Group B Streptococcus – Dorothy L. Ackerman – ACS Infectious Diseases

Review: Development of the gut microbiota in infancy and its impact on health in later life – Masaru Tanaka –  Allergology International

Maternal microbiomes in preterm birth: Recent progress and analytical pipelines – Lindsay A. Parnell – Seminars in Perinatology

Oral microbiology

Application of denaturing gradient gel electrophoresis to the analysis of bacterial communities associated with asymptomatic and symptomatic pericoronitis –  Xin Zhang – Journal of Oral and Maxillofacial Surgery

 

 

Human gut microbiome

Review: Food contact materials and gut health: Implications for toxicity assessment and relevance of high molecular weight migrants – Ksenia J. Groh – Food and Chemical Toxicology

Environmental Pollutant Benzo[a]Pyrene Impacts the Volatile Metabolome and Transcriptome of the Human Gut Microbiota – Clémence Defois – Frontiers in Microbiology

Animal experiments

AvBD1 nucleotide polymorphisms, peptide antimicrobial activities and microbial colonisation of the broiler chicken gut – Kevin Cadwell – BMC Genomics

Increased microbiome diversity at the time of infection is associated with improved growth rates of pigs after co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) – Rebecca A. Ober – Veterinary Microbiology

Changes in the Total Fecal Bacterial Population in Individual Horses Maintained on a Restricted Diet Over 6 Weeks – Kirsty Dougal – Frontiers in Microbiology

Animal microbiome

Analysis of microbiota of the swimming crab (Portunus trituberculatus) in South Korea to identify risk markers for foodborne illness – Suyeon Kim – LWT – Food Science and Technology

Diet and gut microbiota of two supralittoral amphipods Orchestia montagui and Talitrus saltator living in different microhabitats – Khaled F.A. Abdelrhman – Estuarine, Coastal and Shelf Science

Gut microbiome analysis as a tool for developing new probiotic products – Daniel Ramón – Journal of Biotechnology

Review: Human genetic variation and the gut microbiome in disease – Andrew Brantley Hall – Nature Reviews  Genetics

Plant, root, and soil microbiome

Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems – Madangchanok Imchen – Scienfic Reports

Microbial community structure and function respond more strongly to temporal progression than to the application of slurry in an Irish grassland – Aaron Fox – Applied Soil Ecology

Cheating and resistance to cheating in natural populations of the bacterium Pseudomonas fluorescens – John B. Bruce – Evolution

Water and extremophile microbiome

Differences in temperature and water chemistry shape distinct diversity patterns in thermophilic microbial communities – Cecilia M. Chiriac –  Applied nad Environmental Microbiology

Planococcus ruber sp. nov., isolated from a polluted farmland soil sample – Xu Wang – International Journal of Systematic and Evolutionary Microbiology

Microbial diversity in acidic thermal pools in the Uzon Caldera, Kamchatka – Andrey V. Mardanov – Antonie van Leeuwenhoek

Aura-biomes are present in the water layer above coral reef benthic macro-organisms – Kevin Walsh – PeerJ

Physiological and ecological implications of an iron- or hydrogen-oxidizing member of the Zetaproteobacteria, Ghiorsea bivora, gen. nov., sp. nov – Jiro F Mori – The ISME

Food microbiology

Restoration of GABA production machinery in Lactobacillus brevis by accessible carbohydrates, anaerobiosis and early acidification – Qinglong Wu – Food Microbiology

Development of non-pathogenic bacterial biofilms on the surface of stainless steel which are inhibitory to Salmonella enterica – Yoonbin Kim – Food Microbiology

 

Bioinformatics

Metagenome Analysis: a Powerful Tool for Enzyme Bioprospecting – Aravind Madhavan –  Applied Biochemistry and Biotechnology

Novel approaches for bioinformatic analysis of salivary RNA Sequencing data in the biomarker development process – Karolina Elżbieta Kaczor-Urbanowicz – Bioinformatics

Biotechnology

Biogas production from brewery spent grain as a mono-substrate in a two-stage process composed of solid-state anaerobic digestion and granular biomass reactors – Mario Panjičko – Journal of Cleaner Production

Revealing sludge and biofilm microbiomes in membrane bioreactor treating piggery wastewater by non-destructive microscopy and 16S rRNA gene sequencing – Tomohiro Inaba – Chemical Engineering Journal

Techniques

Characterization of syntrophic Geobacter communities using ToF-SIMS – Wenchao Wei – Biointerphases

Labeling of prokaryotic mRNA in live cells using fluorescent in situ hybridization of transcript-annealing molecular beacons (FISH-TAMB) – Rachel Harris – bioRxiv

Microbes in the news

No guts no glory: Harvesting the microbiome of athletes

Oil-eating bacteria help sea life thrive

Tina’s (non-microbiology) picks

 Research project “To Selfie or Not to Selfie” – How Can Scientists Foster Public Trust on Instagram? 

Is there enough transparency in #peerreview? Join the debate #PeerRevWk17

August 17, 2017

After two days of holidays on Microbiome Digest, today our blog is a bit longer with many papers in the part of water, soil and gut microbiome. Moreover, check new tools which can be used to deal with microbiome data (MicrobiomeDB and MetaMeta) and some interesting news about microbes in the “Microbes in the news” section. Enjoy the summer (in the lab or on the beach) while reading what is new in microbial world.

Events and jobs

Quality Control Manager, Microbiology, Technical Operations, Marlborough, Massachusetts, US

Assistant/Associate Professor – Microbiology and Immunology (Job ID #83258), Chicago, US

General microbiome

A macroecological theory of microbial biodiversity – William R. Shoemaker – Nature Ecology & Evolution

Community structure follows simple assembly rules in microbial microcosms – Jonathan Friedman – Nature Ecology & Evolution

Solagigasbacteria: Lone genomic giants among the uncultured bacterial phyla – Eric Becraft – bioRxiv

Review: Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life – Anja Spang – Science

Temperature-Dependent Alkyl Glycerol Ether Lipid Composition of Mesophilic and Thermophilic Sulfate-Reducing Bacteria – Arnauld Vinçon-Laugier – Frontiers in Microbiology

Advances in the analysis of “less-conventional” human body fluids: an overview of the ce- and hplc-ms applications in the years 2015–2017 – Monica Di Venere – Electrophoresis

Pregnancy and early life

Comparison of commercially-available preservatives for maintaining the integrity of bacterial DNA in human milk – Kimberly A.Lackey – Journal of Microbiological Methods

Effects of One-Week Empirical Antibiotic Therapy on the Early Development of Gut Microbiota and Metabolites in Preterm Infants – Danping Zhu – Scientific Reports

Multi-site human microbiome

Genomics-Based Identification of Microorganisms in Human Ocular Body Fluid –  Philipp Kirstahler – bioRxiv

Oral microbiome

Oral microbial community assembly under the influence of periodontitis – Hongju Chen – PLOS One

Subgingival Microbiome of Gingivitis in Chinese Undergraduates – Ke Deng – Chinese Journal of Dental Research

Human skin microbiome

Review: What is new in the pathophysiology of acne, an overview – B. Dréno – Journal of the European Academy of Dermatology and Venerology

The Role of the Skin and Gut Microbiome in Psoriatic Disease – Di Yan – Current Dermatology Reports

Human vaginal microbiome

The Vaginal Microbiome and its Potential to Impact Efficacy of HIV Pre-exposure Prophylaxis for Women –  Jennifer Velloza – Current HIV/AIDS Reports

The urinary microbiota of men and women and its changes in women during bacterial vaginosis and antibiotic treatment – Cornelia Gottschick – Microbiome

 

Human gut microbiome

Interactions between species introduce spurious associations in microbiome studies – Rajita Menon – bioRxiv

Bacteriophages in the gastrointestinal tract and their implications – Marzanna Łusiak-Szelachowska- Gut Pathogens

Analysis of intestinal microbial communities of cerebral infarction and ischemia patients based on high throughput sequencing technology and glucose and lipid metabolism –  Wenzhen Ji – Molecular Medicine Reports

Brain-gut-microbiota axis and mental health – Timothy G. Dinan – Psychosomatic Medicine

Integrated Analysis of Biopsies from Inflammatory Bowel Disease Patients Identifies SAA1 as a Link Between Mucosal Microbes with TH17 and TH22 Cells – Mei San Tang – Inflamatory Bowel Diseases

Gut microbiome response to short-term dietary interventions in reactive hypoglycemia subjects – Sara Quercia –  Diabetes Metabolism Research and Reviews

The Impact of Western Diet and Nutrients on the Microbiota and Immune Response at Mucosal Interfaces – Donjete Statovci –  Frontiers in Immunology

Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects – Elena Buelow – Microbiome

Future prospect of faecal microbiota transplantation as a potential therapy in asthma – Y Kang  – Allergologia et Immunopathologia

Evidence of the Immune Relevance of Prevotella copri, a Gut Microbe, in Patients With Rheumatoid Arthritis – Annalisa Pianta – Arthritis & Rheumatology

Bacteriophages in the gastrointestinal tract and their implications – Marzanna Łusiak-Szelachowska – Gut Pathogens

The impact of age and gut microbiota on Th17 and Tfh cells in K/BxN autoimmune arthritis – Fei Teng – Arthritis Research & Therapy

Amoxapine Demonstrates Incomplete Inhibition of β-Glucuronidase Activity from Human Gut Microbiota – Wei Yang –  SLAS Discovery

Animal experiments 

Role of intestinal microbiome in American ginseng-mediated colon cancer protection in high fat diet-fed AOM/DSS mice –  C.-Z. Wang –  Clinical and Translational Oncology

The influence of the gut microbiota composition on Campylobacter jejuni colonization in chickens – Zifeng Han – Infection and Immunity

Animal microbiome 

Microbiota of little penguins and short-tailed shearwaters during development – Meagan L. Dewar – PLOS One

Transition of the intestinal microbiota of cats with age – Hiroaki Masuoka – PLOS One

Brief Communication: Climate warming reduces gut microbiota diversity in a vertebrate ectotherm – Elvire Bestion – Nature Ecology & Evolution

Patterns of seasonality and group membership characterize the gut microbiota in a longitudinal study of wild Verreaux’s sifakas (Propithecus verreauxi) – Andrea Springer – Ecology and Evolution

Comparison of the microbial population in rabbits and guinea pigs by next generation sequencing – Edward J. Crowley – PLOS One

Effects of contaminants of emerging concern on Megaselia scalaris (Lowe, Diptera: Phoridae) and its microbial community – Marcus J. Pennington – Scientific Reports

Plant, root, and soil microbiome

Influence of heavy metals on rhizosphere microbial communities of Siam weed (Chromolaena odorata (L.)) using a 16S rRNA gene amplicon sequencing approach – Thanyaporn Ruangdech – Agriculture and Natural Resources

Soil microbial community composition is correlated to soil carbon processing along a boreal wetland formation gradient – Eric J. Chapman – European Journal of Soil Biology

Bacteria from the rhizosphere and tissues of As-hyperaccumulator Pteris vittata and their role in arsenic transformation – Yong-HeHan – Chemosphere

Soil Characteristics Overwhelm Cultivar Effects on the Structure and Assembly of Root-Associated Microbiomes of Modern Maize – LinChen – Pedosphere

Comparative Transcriptomics of Bacillus mycoides Strains in Response to Potato-Root Exudates Reveals Different Genetic Adaptation of Endophytic and Soil Isolates – Yanglei Yi – Frontiers in Microbiology

Soil features in rookeries of Antarctic penguins reveal sea to land biotransport of chemical pollutants – Anna C. Santamans – PLOS One

Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism – Elias Broman – Microbiome

Effects of Short-Term Set-Aside Management Practices on Soil Microorganism and Enzyme Activity in China – Guangyu Li – International Journal of Environmental Research and Public Health

Microbial volatile compounds alter the soil microbial community – Jun Yuan –  Environmental Science and Pollution Research

Metagenomes from deep Baltic Sea sediments reveal how past and present environmental conditions determine microbial community composition – Ian P.G. Marshall – Marine Genomics

A More Comprehensive Community of Ammonia-Oxidizing Archaea (AOA) Revealed by Genomic DNA and RNA Analyses of amoA Gene in Subtropical Acidic Forest Soils – Ruo-Nan Wu – Microbial Ecology

Biophysical processes supporting the diversity of microbial life in soil – Robin Tecon – FEMS Microbiology Reviews

Water and extremophile microbiome 

Effect of short-term, diel changes in environmental conditions on active microbial communities in a salt marsh pond – Patrick J. Kearns – Aquatic Microbial Ecology

Linking Phylogenetic Identity and Biogeochemical Function of Uncultivated Marine Microbes with Novel Mass Spectrometry Techniques –  Samuel Bryson – Thesis, Oregon State University

Effects of alkali types on waste activated sludge (WAS) fermentation and microbial communities – Xiaoling Li – Chemosphere

Cyanobacterial Allelochemicals But Not Cyanobacterial Cells Markedly Reduce Microbial Community Diversity – Filipa Dias – Frontiers in Microbiology

Marinobacter aquaticus sp. nov., a moderately halophilic bacterium from a solar saltern –  María José León –  International Journal of Systematic and Evolutionary

Exploring the microbial diversity in Jordanian hot springs by comparative metagenomic analysis – Emad I. Hussein – Microbiology Open

Development of the first gene expression system for Salinicoccus strains with potential application in bioremediation of hypersaline wastewaters – Dahe Zhao – Applied Microbiology and Biotechnology

Bacterial biomes and potential human pathogens in irrigation water and leafy greens from different production systems described using pyrosequencing – M Jongman – Journal of Applied Microbiology

Report: Metabolic Flexibility Underpins Growth Capabilities of the Fastest Growing Alga – Haim Treves – Current Biology

The effects of morphology and neighbouring seaweeds on macroalgal microbiota – Thesis, The University of British Columbia

Relationships between and formation dynamics of the microbiota of consumers, producers, and the environment in an abalone aquatic system – Jing-Zhe Jiang – PLOS One

Vertical gradients in species richness and community composition across the twilight zone in the North Pacific Subtropical Gyre – Stephanie A. Sommer – Molecular Ecology

Metagenomic Insights into The Diversity and Functions of Microbial Assemblages in Tasik Kenyir Ecosystem – Mohd Ezhar Mohd Noor –  bioRxiv

The organizing effects of elevated CO2 on competition among estuarine primary producers – Craig S. Young – Scientific Reports

Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics – Kari M. Finstad – Frontiers in Microbiology

Draft Genome Sequence of Thiohalobacter thiocyanaticus Strain FOKN1, a Neutrophilic Halophile Capable of Thiocyanate Degradation – Mamoru Oshiki – Genome Announcements

Environmental drivers of a microbial genomic transition zone in the ocean’s interior – Daniel R. Mende – Nature Microbiology

Early photosynthetic eukaryotes inhabited low-salinity habitats – Patricia Sánchez-Baracaldo – PNAS

Microbial dynamics in petroleum oilfields and their relationship with physiological properties of petroleum oil reservoirs – Sunita J.Varjani – Bioresource Technology

Probiotics / prebiotics

Label-free quantitative proteomic analysis of Lactobacillus fermentum NCDC 400 during bile salt exposure – Gurjeet Kaur – Journal of Proteomics

Timely Use of Probiotics in Hospitalized Adults Prevents Clostridium difficile Infection: A Systematic Review With Meta-Regression Analysis – Nicole T. Shen – Gastroenterology

Phages and viruses

Phage in urban wastewater have the potential to disseminate antibiotic resistance – Gayathri Upeksha Gunathilaka – International Journal of Antimicrobial Agents

Bioinformatics

MicrobiomeDB: a systems biology platform for integrating, mining and analyzing microbiome experiments – Francislon Silva de Oliveira – bioRxiv

MetaMeta: integrating metagenome analysis tools to improve taxonomic profiling – Vitor C. Piro – Microbiome

A bioarchitectonic approach to the modular engineering of metabolism – Cheryl A. Kerfeld – Philosophical Transactions of the Royal Society B

Techniques

Schrödinger’s microbes: Tools for distinguishing the living from the dead in microbial ecosystems – Joanne B. Emerson – Microbiome

A Note: A simple methodology to collect culturable bacteria from feces of Anopheles darlingi (Diptera: Culicidae) – Andrelisse Arruda – Journal of Microbiological Methods

Biotechnology

Predicting Microbial Fuel Cell Biofilm Communities and Bioreactor Performance using Artificial Neural Networks – Keaton Larson – Environmental Science & Technology

Microbial communities as biosensors for monitoring urban environments – Fangqiong Ling – Microbial Biotechnology

Perspectives for microbial community composition in anaerobic digestion: from abundance and activity to connectivity – Jo De Vrieze – Environmental Microbiology

Review: Purification and reuse of non-point source wastewater via Myriophyllum-based integrative biotechnology: A review – Liu F – Bioresource Technology

Improvements in algal lipid production: a systems biology and gene editing approach –  Avik Banerjee – Critical Reviews in Biotechnology

Microbes in the news 

Scientists Make Food From Bacteria, Water, Electricity, and a Whole Lot of Patience

Are you lonesome tonight? Why we, like Elvis, turn to food for comfort

Scientists See Bacteria Responding Electrically to Physical Stimuli for the First Time

Killing bacteria by hacking plastics with silver and electricity

Human Gut Microbes May Help Suppress MS, New Research Suggests 

Unexpected Microbial Life in Glacial Clay Could Offer Antibiotic Solutions

 

 

 

August 1, 2017

Today’s digest is relatively short, but there is an amazing commentary on rhizosheath and advantages of using phylogenetic distances to examine the microbial communities

Human gut microbiome

Maternal modifiers of the infant gut microbiota: metabolic consequences

Mulligan CM. Journal of Endocrinology

Association between gut microbiota and bone health: potential mechanisms and prospective

Chen YC. The Journal of Clinical Endocrinology & Metabolism

Plant, soil, and air microbiome

Amynthas agrestis invasion increases microbial biomass in Mid-Atlantic deciduous forests

Chang CH. Soil Biology and Biochemistry

Effect of nanoparticles on crops and soil microbial communities

Rajput VD. Journal of Soils and Sediments

Bottom-up effects on herbivore-induced plant defences: a case study based on compositional patterns of rhizosphere microbial communities.

Benítez E. Scientific reports

Unwrapping the rhizosheath

Pang J. Plant and Soil

Marine and inland waters

Marine archaea and archaeal viruses under global change

Danovaro R-F1000 Research

Bacterial community structure in the intertidal biofilm along the Yangtze Estuary, China

Guo X .Marine Pollution Bulletin

Fronts at the surface ocean can shape distinct regions of microbial activity and community assemblages down to the bathypelagic zone: The Azores Front as a case study

Baltar F. Frontiers in Marine Science

Microbiome Approaches/Techniques

A deep metaproteomics approach for the study of human microbiomes

Zhang X Analytical Chemistry, 2017

Advantages of phylogenetic distance based constrained ordination analyses for the examination of microbial communities.

Shankar V. Scientific reports

Oral/Nasal Microbiome 

The periodontal war: microbes and immunity

Ebersole JL. PERIODONTOLOGY 2000

Design and validation of a DNA-microarray for phylogenetic analysis of bacterial communities in different oral samples and dental implants

Parolin C. Scientific Reports

Influence of the pneumococcal conjugate vaccines on the temporal variation of pneumococcal carriage and the nasal microbiota in healthy infants: a longitudinal analysis of a case–control study

Mika M. Microbiome

Food Microbiology 

Comparison study of the volatile profiles and microbial communities of Wuyi Qu and Gutian Qu, two major types of traditional fermentation starters of Hong Qu glutinous rice wine

Liu Z.Food Microbiology

Plant-mediated restriction of Salmonella enterica on tomato and spinach leaves colonized with Pseudomonas plant growth-promoting rhizobacteria

Hsu CK.International Journal of Food Microbiology, 2017

July 23, 2017

General microbiome

Systems biology of lactic acid bacteria: For food and thought – Bas Teusink, Current Opinion in Systems Biology

Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta) – Susan H. Brawley, PNAS

Parasite Microbiome Project: Systematic Investigation of Microbiome Dynamics within and across Parasite-Host Interactions – Nolwenn M. Dheilly, mSystems

Human respiratory microbiome

Airway microbiota signals anabolic and catabolic remodeling in the transplanted lung – Stéphane Mouraux, Journal of Allergy and Clinical Immunology

Human skin microbiome

The Skin Microbiome of Cohabiting Couples – Ashley A. Ross, mSystems

Human oral microbiome

Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules – Anna Edlund, mSystems

Human gut microbiome

Sequencing the gut metagenome as a non-invasive diagnosis for advanced nonalcoholic steatohepatitis – Lixin Zhu, Hepatology

Molecular Characterization of the Human Stomach Microbiota in Gastric Cancer Patients – Guoqin Yu, Frontiers in Microbiology

Inulin-type fructans and whey protein both modulate appetite but only fructans alter gut microbiota in adults with overweight/obesity: a randomized controlled trial – Raylene A. Reimer, Molecular Research and Food Research

Incomplete metabolism of phytoestrogens by gut microbiota from children under the age of three – Pilar Gaya, International Journal of Food Sciences and Nutrition

Animal experiments

An In Vitro Chicken Gut Model Demonstrates Transfer of a Multidrug Resistance Plasmid from Salmonella to Commensal Escherichia coli – Roderick M. Card, mBio

Maternally-transmitted microbiota affects odor emission and preference in Drosophila larva – Jean-Pierre Farine, Scientific Reports

Burn Injury Leads to Increase in Relative Abundance of Opportunistic Pathogens in the Rat Gastrointestinal Microbiome – Guangtao Huang, Scientific Reports

Linking Sex Differences in Non-Alcoholic Fatty Liver Disease to Bile Acid Signaling, Gut Microbiota, and High Fat Diet  – John Y.L. Chiang, The American Journal of Pathology

Early-life disruption of amphibian microbiota decreases later-life resistance to parasites – Sarah A. Knutie, Nature Communication

In vitro characteristics of an Atlantic salmon (Salmo salar L.) hind gut microbial community in relation to different dietary treatments – Kamarul Zaman Zarkasia,  Research in Microbiology

Effects of coconut oil on glycemia, inflammation, and urogenital microbial parameters in female Ossabaw mini-pigs – Annie E. Newell-Fugate, PLoS ONE

Effect of acute ozone exposure on the lung metabolomes of obese and lean mice – Joel Andrew Mathews, PLoS ONE

Animal microbiome

Skin Bacterial Community Reorganization Following Metamorphosis of the Fire-Bellied Toad (Bombina orientalis) – Arnaud Bataille, Microbial Ecology

Inferring microbial interactions in thermophilic and mesophilic anaerobic digestion of hog waste – Grace Tzun-Wen Shaw, PLoS ONE

Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation – Olov Svartström, ISME

Genome Sequences of Two Shewanella spp. Isolated from the Gut of the Sea Cucumber Apostichopus japonicus (Selenka, 1867) – Hyun-Hee Hong, Genome Anouncements

Feather-Degrading Bacteria: Their Biochemical and Genetic Characteristics – Paweł Kowalczyk, Arabian Journal for Science and Engineering

Plant, root, and soil microbiome

The tree species matters: Belowground carbon input and utilization in the myco-rhizosphere – Janine Sommera, European Journal of Soil Biology

Soil bacterial community response to vegetation succession after fencing in the grassland of China – Quanchao Zeng, Science of The Total Environment

Drought Stress Results in a Compartment-Specific Restructuring of the Rice Root-Associated Microbiomes – Christian Santos-Medellín, mBio

Improved grain yield of cowpea (Vigna unguiculata) under water deficit after inoculation with Bradyrhizobium elkaniiand Rhizophagus irregularis – Rui S. Oliveira, Crop and Pasture Science

Understanding the holobiont: the interdependence of plants and their microbiome – Carmen Sánchez-Cañizares, Current Opinion in Microbiology

Pseudomonas fluorescens R68 assisted enhancement in growth and fertilizer utilization of Amaranthus tricolor (L.) – C. Jimtha John, 3Biotech

Ecological guild and enzyme activities of rhizosphere soil microbial communities associated with Bt-maize cultivation under field conditions in North West Province of South Africa – Deidré A. B. van Wyk, Journal of Basic Microbiology

A genomic perspective on stoichiometric regulation of soil carbon cycling – Wyatt H Hartman, ISME

The rhizosphere microbiome of burned holm-oak: potential role of the genus Arthrobacter in the recovery of burned soils – Antonio J. Fernández-González, Scientific Reports

Biological control of potential antagonistic bacteria isolates to restrict Magnaporthe grisea infection on rice – David P. Tokpah, African Journal of Microbiology Research

Bacteria associated to plants naturally selected in a historical PCB polluted soil show potential to sustain natural attenuation – Lorenzo Vergani, Frontiers in Microbiology

Water and extremophile microbiome

Unraveling the Microbial Interactions and Metabolic Potentials in Pre- and Post-treated Sludge from a Wastewater Treatment Plant Using Metagenomic Studies – Chandni Sidhu, Frontiers in Microbiology

Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China – Jian-Qiang Su, Microbiome

Microbial Community Structure and Function Decoupling Across a Phosphorus Gradient in Streams – Erick S. LeBrun, Microbial Ecology

Microbial communities and their predicted metabolic functions in growth laminae of a unique large conical mat from Lake Untersee, East Antarctica – Hyunmin Koo, Frontiers in Microbiology

Draft genome sequence of Exiguobacterium aurantiacumstrain PN47 isolate from saline ponds, known as “Salar del Huasco”, located in the Altiplano in the North of Chile – Erwin Strahsburger, Brazilian Journal of Microbiology

Diversity of culturable filamentous Ascomycetes in the eastern South Pacific Ocean off Chile – Jeanett Vera, World Journal of Microbiology and Biotechnology

Salinity Drives the Virioplankton Abundance but Not Production in Tropical Coastal Lagoons – Pedro C. Junger, Microbial Ecology

Characterization of a cold-adapted DNA photolyase from C. psychrerythraea 34H – Sudipto Munshi, Extremophiles

Marine archaeal dynamics and interactions with the microbial community over 5 years from surface to seafloor – Alma E Parada, ISME

Unusual metabolic diversity of hyperalkaliphilic microbial communities associated with subterranean serpentinization at The Cedars – Shino Suzuki, ISME

Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept – Melissa B. Duhaime, Frontier in Microbiology

Effects of Physiochemical Factors on Prokaryotic Biodiversity in Malaysian Circumneutral Hot Springs – Chia S. Chan, Frontiers in Microbiology

Climate oscillations reflected within the microbiome of Arabian Sea sediments – William D. Orsi, Scientific Reports

Microbiome of Trichodesmium Colonies from the North Pacific Subtropical Gyre – Mary R. Gradoville, Frontiers in Microbiology

Antarctic sea ice region as a source of biogenic organic nitrogen in aerosols – Manuel Dall’Osto, Scientific Reports

Built environment

A role for microbial selection in frescoes’ deterioration in Tomba degli Scudi in Tarquinia, Italy – Maria Cristina Tomassetti, Scientific Reports

Food microbiology

An Exploration into the Bacterial Community under Different Pasteurization Conditions during Substrate Preparation (Composting–Phase II) for Agaricus bisporus Cultivation – Fabricio Rocha Vieira, Microbial Ecology

Metagenome-based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments – Conor J Doyle, Environmental Microbiology

Draft Genome Sequences of Three Lactobacillusparacasei Strains, Members of the Nonstarter Microbiota of Mature Cheddar Cheese – Ewelina Stefanovic, Genome Anouncements

Bioinformatics

Cohesion: a method for quantifying the connectivity of microbial communities – Cristina M Herren, ISME

Developing integrative systematics in the informatics and genomic era, and calling for a global Biodiversity Cyberbank – Jun Wen, Journal of Systematics and Evolution

Techniques

Rapid differentiation of bacterial communities using high resolution melting analysis – Steven Everman, Journal of Microbiological Methods

Proteomics in Inflammatory Bowel Disease: Approach Using Animal Models – Fadi H. Mourad, Digestive Diseases and Sciences

June 23, 2017

Human Microbiome

Genome reconstruction and characterisation of extensively drug-resistant bacterial pathogens through direct metagenomic sequencing of human faeces – Mu et al. – BioRxiv

Oropharyngeal and Sputum Microbiomes Are Similar Following Exacerbation of Chronic Obstructive Pulmonary Disease – Liu et al. – Frontiers in Microbiology

Segal’s Law, 16S rRNA gene sequencing, and the perils of foodborne pathogen detection within the American Gut Project – Pettengill & Rand – PeerJ

Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis – Tett et al. – npj Biofilms and Microbiomes

Rosacea and its association with enteral microbiota in Korean females – Nam et al. – Experimental Dermatology

Review: The role of microbiota, and probiotics and prebiotics in skin health – Maguire & Maguire – Archives of Dermatological Research

Human age and skin physiology shape diversity and abundance of Archaea on skin – Moissl-Eichinger et al. – Scientific Reports

Microbial Signatures Associated with Oropharyngeal and Oral Squamous Cell Carcinomas – Banerjee et al. – Scientific Reports

 

Animal Microbiome

Gut Dysbiosis and Adaptive Immune Response in Diet-induced Obesity vs. Systemic Inflammation – Pindjakova et al. – Frontiers in Microbiology

Characterization of the Microbiome along the Gastrointestinal Tract of Growing Turkeys Wilkinson et al. – Frontiers in Microbiology

Diet-induced reconstruction of mucosal microbiota associated with alterations of epithelium lectin expression and regulation in the maintenance of rumen homeostasis – Shen et al. – Scientific Reports

Fatty acid composition and phospholipid types used in infant formulas modifies the establishment of human gut bacteria in germ-free mice –  Guldhammer Nejrup et al. – Scientific Reports

Microbiota-derived butyrate suppresses group 3 innate lymphoid cells in terminal ileal Peyer’s patches – Kim et al. – Scientific Reports

Early-life gut microbial colonization shapes Th1/Th2 balance in asthma model in BALB/c mice – Qin et al. – BMC Microbiology

The development of lower respiratory tract microbiome in mice – Singh et al. – Microbiome (BMC)

 

Pathogen research

Genetic indicators of drug resistance in the highly repetitive genome of Trichomonas vaginalis – Bradic et al. – Genome Biology and Evolution

Metabolic and fitness determinants for in vitro growth and intestinal colonization of the bacterial pathogen Campylobacter jejuni – Gao et al. – PLoS Biology

Review: Periodontal diseases – Kinane et al. – Nature Reviews Disease Primer

 

Soil and Water Microbiome

Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge – McIlroy et al. – Frontiers in Microbiology

Nitrogen enrichment impacts on boreal litter decomposition are driven by changes in soil microbiota rather than litter quality – Maaroufi et al. – Scientific Reports

 

Bioinformatics

CD-HIT-OTU-MiSeq, an Improved Approach for Clustering and Analyzing Paired End MiSeq 16S rRNA Sequences – Li et al. – BioRxiv

Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments – Yim​ & Cushman – PeerJ

BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters – Cheng et al. – PeerJ Preprints

 

Evolution

Phylogenetic Tracings of Proteome Size Support the Gradual Accretion of Protein Structural Domains and the Early Origin of Viruses from Primordial Cells – Nasir et al. – Frontiers in Microbiology

Pan-genome and phylogeny of Bacillus cereus sensu lato – Bazinet – BioRxiv

TreeTime: maximum likelihood phylodynamic analysis – Sagulenko et al. – BioRxiv

 

Other

Review: Fungal and Bacterial Pigments: Secondary Metabolites with Wide Applications –  Morris et al. – Frontiers in Microbiology

A Highly Efficient CRISPR-Cas9-Mediated Large Genomic Deletion in Bacillus subtilis – So et al. – Frontiers in Microbiology

April 19, 2017

Exciting papers with locoregional effects of microbiota in a mouse model of colon carcinogenesis, maternal high fat diet detrimentally alterring epigenetic and gut microbiome pathways leading to fatty liver disease in mice.

Events and jobs

ASM Microbe 2017 : New Orleans

QC Microbiology Product Testing Associate – Experis : Irvine, CA
General microbiome

Review: Applying the design-build-test paradigm in microbiome engineering – Hoang Long Pham – Current Opinion in Biotechnology

Cohort Profile: African Collaborative Center for Microbiome and Genomics Research’s (ACCME) Human Papillomavirus (HPV) and Cervical Cancer Study – Sally N. Adebamowo – International Journal of Epidemiology

Review: Cultured microbes represent a substantial fraction of the human and mouse gut microbiota – Ilias Lagkouvardos – Gut Microbes

Human skin microbiome

A distinct cutaneous microbiota pofile in autoimmune bullous disease patients – Mor Miodovnika – Experimental Dermatology

Human gut microbiome

Review : A psychology of the human brain–gut–microbiome axis – Andrew P. Allen – Social and Personality Psychology Compass

Multivariate modelling of faecal bacterial profiles of patients with IBS predicts responsiveness to a diet low in FODMAPs – Sean M P Bennet – Gut

Animal microbiome

Temporal changes in cutaneous bacterial communities of terrestrial- and aquatic- phase newts (Amphibia) – Joana Sabino-Pinto – Environmental Microbiology

The low diverse gastric microbiome of the jellyfish Cotylorhiza tuberculata is dominated by four novel taxa – Tomeu Viver – Environmental Microbiology

Studying the effect of administration route and treatment dose on the selection of enrofloxacin resistance in commensal Escherichia coli in broilers – Ilias Chantziaras -Journal of Antimicrobial Chemotherapy

The skin microbiome of the Common thresher shark (Alopias vulpinus) has low taxonomic and potential metabolic β-diversity – Michael P. Doane – Environmental Microbiology Reports

Animal experiments

Intestinal, extra-intestinal and systemic sequelae of Toxoplasma gondii induced acute ileitis in mice harboring a human gut microbiota – Eliane von Klitzing – PLOS ONE

Effects of the inclusion of a Bacillus direct-fed microbial on performance parameters, bone quality, recovered gut microflora, and intestinal morphology in broilers consuming a grower diet containing corn distillers dried grains with solubles – J. D. Latorre – Poultry Science

Effect of high-fat diet and growth stage on the diversity and composition of intestinal microbiota in healthy bovine livestock – Shengyin Jiao – Journal of the Science of Food and Agriculture

*Locoregional effects of microbiota in a preclinical model of colon carcinogenesis – Sarah Tomkovich – Cancer Research

Selection of Cholesterol-Lowering Lactic Acid Bacteria and its Effects on Rats Fed with High-Cholesterol Diet – Yufang Liu – Current Microbiology

*Enhanced offspring predisposition to steatohepatitis with maternal high-fat diet is associated with epigenetic and microbiome alterations – Umesh D. Wankhade – PLOS ONE

Plant, root, and soil microbiome

Archaea and bacteria mediate the effects of native species root loss on fungi during plant invasion – Steven D Mamet- The ISME Journal

An acid-tolerant ammonia-oxidizing γ-proteobacterium from soil – Masahito Hayatsu – The ISME Journal

Investigation of Arsenotrophic Microbiome in Arsenic-Affected Bangladesh Groundwater – Munawar Sultana – Groundwater

Unexpected associated microalgal diversity in the lichen Ramalina farinacea is uncovered by pyrosequencing analyses – Patricia Moya – Plos ONE

Tuber indicum shapes the microbial communities of ectomycorhizosphere soil and ectomycorrhizae of an indigenous tree (Pinus armandii) – Qiang Li – Plos ONE

The ‘known’ genetic potential for microbial communities to degrade organic phosphorus is reduced in low-pH soils – Ian D. E. A. Lidbury – Microbiology Open

Shifting microbial communities sustain multiyear iron reduction and methanogenesis in ferruginous sediment incubations – M. S. Bray – Gebiology

Water and extremophile microbiome

Discovery of anaerobic lithoheterotrophic haloarchaea, ubiquitous in hypersaline habitats – Dimitry Y Sorokin – The ISME Journal

Cultivation and characterization of Candidatus Nitrosocosmicus exaquare, an ammonia-oxidizing archaeon from a municipal wastewater treatment system – Laura A Sauder – The ISME Journal

Minireview: Microbial ecology of mountain glacier ecosystems: Biodiversity, ecological connections, and implications of a warming climate – Scott Hotaling – Environmental Microbiology

Probiotics / prebiotics
Colonic gas homeostasis: Mechanisms of adaptation following HOST-G904 galactooligosaccharide use in humans – M. Mego – Neurogastroenterology and Motility

Techniques

Stochastically reduced communities—Microfluidic compartments as model and investigation tool for soil microorganism growth in structured spaces – Jialan Cao – Engineering in Life Sciences

Protocol : Metagenomics and CAZyme Discovery – Benoit J. Kunath – Protein-Carbohydrate Interactions : Methods in Molecular Biology

The resident microflora of voided midstream urine of healthy controls: standard versus expanded urine culture protocols – L. Coorevits – European Journal of Clinical Microbiology & Infectious Diseases

Microbes in the news

Study finds amoeba ‘grazing,’ killing bacteria usually protected by film

How Bacteria-Laden Beetle Poop Is Killing American Squash and Melons

Glowing bacteria detect buried landmines

Science, publishing, and career

Saturday, Science Advocates Prepare for a Long March

Anitha’s non-microbiology picks

Research unlocks molecular key to animal evolution and disease

Cumulative culture can emerge from collective intelligence in animal groups – Takao Sasaki – Nature Communications

March 9, 2017

A variety of reviews about the oral microbiome and periodontal disease, a perspective piece on secondary metabolites mediating symbiotic interactions in the new Nature Reviews Chemistry journal, Akkermansia muciniphila’s involvement in host immune homeostasis, new insight into how raindrops disperse bacteria from soil into the air.

General microbiome

* Perspective: Hijacking exogenous signals to generate new secondary metabolites during symbiotic interactions – Rurun Wang – Nature Reviews Chemistry

Cooperation of Gastric Mononuclear Phagocytes with Helicobacter pylori during Colonization – Monica Viladomiu – Journal of Immunology

Human respiratory microbiome

Longitudinal sampling of the lung microbiota in individuals with cystic fibrosis – Fiona J. Whelan – PLoS ONE

Human oral microbiome

Review: Role of microbial communities in the pathogenesis of periodontal diseases and caries – Alex Mira – Journal of Clinical Periodontology

Review: Dental biofilm: ecological interactions in health and disease – P. D. Marsh – Journal of Clinical Periodontology

Review: The oral cavity microbiota: between health, oral disease and cancers of the aerodigestive tract – Pierre Le Bars – Canadian Journal of Microbiology

A new mathematical model of bacterial interactions in two-species oral biofilms – Bénédicte Martin – PLoS ONE

Human urinary microbiome

Alterations of Urinary Microbiota in Type 2 Diabetes Mellitus with Hypertension and/or Hyperlipidemia – Fengping Liu – Frontiers in Physiology

Human gut microbiome

Impact of Bariatric Surgery on Metabolic and Gut Microbiota Profile: a Systematic Review and Meta-analysis – Dimitrios E. Magouliotis – Obesity Surgery

Commensal gut bacteria modulate phosphorylation-dependent PPARγ transcriptional activity in human intestinal epithelial cells – Malgorzata Nepelska – Scientific Reports

* Pili-like proteins of Akkermansia muciniphila modulate host immune responses and gut barrier function – Noora Ottman – PLoS ONE

Altered intestinal microbiota in patients with chronic pancreatitis: implications in diabetes and metabolic abnormalities – Sai Manasa Jandhyala – Scientific Reports

Disease-Associated Changes in Bile Acid Profiles and Links to Altered Gut Microbiota – Susan A. Joyce – Digestive Diseases

One-year calorie restriction impacts gut microbial composition but not its metabolic performance in obese adolescents – Alicia Ruiz – Environmental Microbiology

Dysbiosis of Gut Microbiota Associated with Clinical Parameters in Polycystic Ovary Syndrome – Rui Liu – Frontiers in Microbiology

Animal experiments

Bifidobacterium breve with α-linolenic acid alters the composition, distribution and transcription factor activity associated with metabolism and absorption of fat – Elaine Patterson – Scientific Reports

Exploring gastric bacterial community in young pigs – Vincenzo Motta – PLoS ONE

Animal microbiome

Parasitism perturbs the mucosal microbiome of Atlantic Salmon – M. S. Llewellyn – Scientific Reports

The microbiome composition of Aedes aegypti is not critical for Wolbachia-mediated inhibition of dengue virus – Michelle D. Audsley – PLoS Neglected Tropical Diseases

Endosymbiotic calcifying bacteria across sponge species and oceans – Leire Garate – Scientific Reports

Bacterial communities associated with Shinkaia crosnieri from the Iheya North, Okinawa Trough: Microbial diversity and metabolic potentials – Jian Zhang – Journal of Marine Systems

Diet affects arctic ground squirrel gut microbial metatranscriptome independent of community structure – Jasmine J. Hatton – Environmental Microbiology

Plant, root, and soil microbiome

Microbial Communities as Environmental Indicators of Ecological Disturbance in Restored Carbonate Fen-Results of 10 Years of Studies – Tomasz Mieczan – Microbial Ecology

Rhizospheric microbial community of Caesalpinia spinosa (Mol.) Kuntze in conserved and deforested zones of the Atiquipa fog forest in Peru – Irene Cordero – Applied Soil Ecology

Abundance and diversity of ammonia-oxidizing archaea and bacteria in the rhizosphere soil of three plants in the Ebinur Lake wetland – Yuan He – Canadian Journal of Microbiology

Alphaproteobacteria fix nitrogen in a Sphagnum-dominated peat bog using molybdenum-dependent nitrogenase – Melissa J. Warren – bioRxiv

Water and extremophile microbiome

Quantifying the importance of the rare biosphere for microbial community response to organic pollutants in a freshwater ecosystem – Yuanqi Wang – Applied and Environmental Microbiology

Comparison of Prokaryotic Diversity in Cold, Oligotrophic Remote Lakes of Chilean Patagonia – Paulina Aguayo – Current Microbiology

Plasmid DNA analysis of pristine groundwater microbial communities reveal extensive presence of metal resistance genes – Ankita Kothari – bioRxiv

Food microbiology

Characterization of microbial population of breba and main crops (Ficus carica) during cold storage: Influence of passive modified atmospheres (MAP) and antimicrobial extract application – María del Carmen Villalobos – Food Microbiology

Genetic diversity, safety and technological characterization of lactic acid bacteria isolated from artisanal Pico cheese – M. F. P. Domingos-Lopes – Food Microbiology

Probiotics/prebiotics

A proliferative probiotic Bifidobacterium strain in the gut ameliorates progression of metabolic disorders via microbiota modulation and acetate elevation – Ryo Aoki – Scientific Reports

More microbes

* Bioaerosol generation by raindrops on soil – Young Soo Joung – Nature Communications

Cooperation in carbon source degradation shapes spatial self-organization of microbial consortia on hydrated surfaces – Robin Tecon – Scientific Reports

Microbes in the news

The ‘Dark Matter’ of the Microbial World – Sarah Zhang – The Atlantic

Scientists Make Art From Objects Invisible to the Naked Eye – Marissa Fessenden – Smithsonian